I can confirm (that this is a pain).

1) Use xprops to find the proper WM_CLASS for your running application (e.g. 
downloaded jar, JabRef in my case).
2) From comment #16, add the proper tag to your desktop file: 
"StartupWMClass=<WM_CLASS>" (modify according to results of 1). This does not 
work yet. Actually, the app shows up for 1s and disappeared. Previously, 
without the startupwmclass tag, it was a void icon (nothing display), that did 
not work either. The trick is:
3) Put that desktop entry into your launcher, log out, log in.

I was able to hit the icon shortly before it disappeared, which crashed
compiz *g*. Without compiz the icon did not disappear and right-click >
keep in launcher worked fine. After relog, compiz works again and the
icon too. Alternatively, it could work to drag&drop the desktop file to
the launcher (which had no effect on my system - zero sized icon
eventually?) and relog.

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https://bugs.launchpad.net/bugs/757991

Title:
  java applications a double icon appears

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